[English] 日本語
Yorodumi
- PDB-4f2n: Crystal structure of iron superoxide dismutase from Leishmania major -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f2n
TitleCrystal structure of iron superoxide dismutase from Leishmania major
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / SSGCID / NIH / NIAID / SBRI / Emerald Biostructures / Structural Genomics / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / mitochondrion / metal ion binding
Similarity search - Function
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Iron superoxide dismutases in eukaryotic pathogens: new insights from Apicomplexa and Trypanosoma structures.
Authors: Phan, I.Q. / Davies, D.R. / Moretti, N.S. / Shanmugam, D. / Cestari, I. / Anupama, A. / Fairman, J.W. / Edwards, T.E. / Stuart, K. / Schenkman, S. / Myler, P.J.
History
DepositionMay 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Superoxide dismutase
B: Superoxide dismutase
C: Superoxide dismutase
D: Superoxide dismutase
E: Superoxide dismutase
F: Superoxide dismutase
G: Superoxide dismutase
H: Superoxide dismutase
I: Superoxide dismutase
J: Superoxide dismutase
K: Superoxide dismutase
L: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,93924
Polymers313,26912
Non-polymers67012
Water25,6171422
1
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3234
Polymers52,2112
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-7 kcal/mol
Surface area17570 Å2
MethodPISA
2
C: Superoxide dismutase
D: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3234
Polymers52,2112
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-6 kcal/mol
Surface area17380 Å2
MethodPISA
3
E: Superoxide dismutase
F: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3234
Polymers52,2112
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-7 kcal/mol
Surface area17480 Å2
MethodPISA
4
G: Superoxide dismutase
H: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3234
Polymers52,2112
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-7 kcal/mol
Surface area17410 Å2
MethodPISA
5
I: Superoxide dismutase
J: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3234
Polymers52,2112
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-7 kcal/mol
Surface area17540 Å2
MethodPISA
6
K: Superoxide dismutase
L: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3234
Polymers52,2112
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-5 kcal/mol
Surface area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.030, 102.740, 168.240
Angle α, β, γ (deg.)91.66, 96.36, 95.01
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Superoxide dismutase / / iron superoxide dismutase


Mass: 26105.736 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: FESODA, LMJF_08_0290 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4QIE0, superoxide dismutase
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1422 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: EBS internal tracking number 232906f2, LemaA.01199.b.A2_PW34974 at 35.33 mg/mL in 25 mM HEPES, pH 7.0, 500 mM sodium chloride, 2 mM DTT, 0.025% sodium azide, 5% glycerol, 0.4 uL + 0.4 uL ...Details: EBS internal tracking number 232906f2, LemaA.01199.b.A2_PW34974 at 35.33 mg/mL in 25 mM HEPES, pH 7.0, 500 mM sodium chloride, 2 mM DTT, 0.025% sodium azide, 5% glycerol, 0.4 uL + 0.4 uL drop with 18.4% PEG3350, 184 mM potassium formate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976484 / Wavelength: 0.976484 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2012
RadiationMonochromator: Asymmetric curved crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976484 Å / Relative weight: 1
ReflectionResolution: 1.85→19.774 Å / Num. obs: 256038 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.63 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 17.65
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.8 / % possible all: 91.5

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ISA
Resolution: 1.85→19.774 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.222 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.203 12890 5 %RANDOM
Rwork0.173 ---
obs0.175 256038 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å2-0.02 Å2-2.07 Å2
2---1.4 Å2-0.12 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20026 0 12 1422 21460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0220752
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.92728269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80552525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96124.105994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.594153200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.851572
X-RAY DIFFRACTIONr_chiral_restr0.0890.22962
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116220
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 900 -
Rwork0.263 17111 -
obs--91.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.1804-4.8408-2.44488.69651.80848.3681-0.07470.2674-0.5021-0.1848-0.22650.81180.4008-0.10790.30120.1399-0.0402-0.05470.1437-0.04410.185-19.1281-23.6523-96.1518
21.91071.45340.40643.53690.04140.96340.07720.2414-0.0581-0.3599-0.0724-0.26390.14140.3308-0.00480.1110.02630.05830.2341-0.00610.10710.1049-22.4164-93.3036
31.31690.24150.05112.2532-0.07051.39990.1490.0561-0.158-0.037-0.03390.08390.19830.0137-0.11510.1103-0.0199-0.0260.1259-0.00730.1277-11.9911-29.8373-87.9884
41.8871-0.58380.07362.06470.04491.5725-0.02970.12010.212-0.1547-0.04640.0404-0.2428-0.00960.07610.1035-0.0213-0.00250.10970.02150.1184-15.316-3.2144-89.7597
51.1753-0.36550.67171.0032-0.16640.8835-0.00170.00420.0577-0.063-0.01170.012-0.03990.02010.01340.0623-0.02450.020.13310.01090.119-11.0237-12.6167-84.8736
60.40150.4326-0.42971.8859-1.67741.9928-0.1789-0.13720.05180.16270.0516-0.199-0.21130.17930.12720.23350.0229-0.09290.2094-0.03830.15796.9618-15.7347-53.457
71.73570.0958-0.90960.7168-0.40762.0323-0.08510.0390.07590.1970.0477-0.1155-0.2456-0.0760.03750.0985-0.0192-0.03010.1219-0.00590.12711.7071-14.6669-61.483
80.5851-0.18590.1391.7729-0.60151.3942-0.00670.0468-0.02520.0319-0.0516-0.2150.15080.16130.05840.05010.00840.01470.1435-0.00180.159410.5475-33.9578-64.3643
92.03320.3537-0.37134.70960.619814.2687-0.1109-0.01940.02170.4081-0.03260.12820.3285-0.41960.14350.0728-0.00280.03190.12030.02010.13411.6668-37.4416-55.9889
100.3319-0.38720.15650.77-0.14871.5933-0.04060.065-0.00740.0890.0034-0.17010.04540.12030.03720.0438-0.0223-0.00340.14650.00870.16368.1248-26.6484-65.4918
111.3816-0.2724-0.33754.42730.49391.9464-0.1037-0.0330.04630.2697-0.0128-0.3892-0.08130.33910.11650.1533-0.028-0.10.14530.02810.082417.646228.539-135.7428
120.8191-0.5942-0.29531.75930.22561.96130.03630.03070.11360.1309-0.0459-0.195-0.36430.12510.00970.1464-0.0296-0.04470.10130.00640.085911.706136.6032-140.9607
130.43050.3085-0.09510.7463-0.14331.42450.0394-0.0585-0.01250.1761-0.1025-0.15090.00380.13040.06310.1848-0.0086-0.04820.13130.00120.112311.217522.5072-136.7893
141.7590.1955-1.21145.0249-2.84916.07630.1289-0.0614-0.04290.1207-0.08790.06190.34630.0562-0.0410.2124-0.0422-0.05160.0757-0.03390.09363.30998.487-139.8753
150.2689-0.03990.19451.3954-0.5951.77880.05120.026-0.04710.1621-0.057-0.01250.0862-0.01020.00590.1615-0.0008-0.01770.1003-0.00770.09587.254519.5744-140.9546
162.7678-0.84691.26643.2582-0.48441.01760.10160.4287-0.0551-0.3670.0585-0.07490.40880.1683-0.16010.35310.0055-0.08040.1721-0.04490.1008-2.855222.6502-175.7097
172.5274-0.18540.19121.3147-0.24061.15530.18410.0592-0.1769-0.2203-0.03010.09410.35780.0219-0.1540.1920.0185-0.03250.0849-0.02670.0858-1.724921.5988-166.3434
181.6064-0.96410.41913.524-0.1071.84910.12980.1170.2627-0.4076-0.1316-0.135-0.12040.120.00180.08490.02020.06530.16380.01770.11144.189944.4865-174.0543
190.44510.03410.461.42-0.54050.97090.08570.02540.0437-0.0953-0.0789-0.00040.07460.105-0.00680.0960.03170.03730.1503-0.01170.10243.039535.9015-165.0579
2014.39243.8796-0.76167.7035-1.57280.3244-0.18070.63150.1772-0.49280.19960.06690.1237-0.0261-0.01890.24960.0287-0.05410.14880.00850.0566-6.565839.1814-179.2437
217.0924-0.67455.51843.5476-0.98797.76110.2507-0.1811-0.62410.34110.15780.31540.4263-0.4677-0.40850.1084-0.05150.05140.09620.04380.2533-12.1138-47.9946-159.6515
222.00240.6423-0.5522.31670.29412.42040.0232-0.0513-0.2630.25350.1201-0.31080.34630.2193-0.14330.09030.025-0.00270.12030.00960.2427-0.2533-41.6201-160.376
230.71910.29140.72392.28140.13772.3233-0.03210.0127-0.1023-0.0550.02770.1513-0.0349-0.05360.00440.0151-0.00920.03970.12580.00660.1727-11.2568-33.954-168.3339
240.87460.3140.80292.71070.4071.5173-0.04940.0095-0.0024-0.07720.04050.1619-0.1588-0.10890.00890.0385-0.00690.04340.15920.00540.1649-8.7137-28.2942-165.7907
259.61783.4027-1.79912.6789-0.39132.8581-0.12670.1233-0.3132-0.57110.02890.2870.3432-0.07930.09780.2754-0.0177-0.08260.1815-0.0260.3021-14.157-40.0788-174.6668
260.30860.3089-0.35812.69441.26422.332-0.0585-0.02070.0634-0.19160.1346-0.2517-0.51290.198-0.07610.3235-0.0544-0.08930.08930.00710.16945.4456-1.7398-150.7967
271.6676-0.5814-0.30122.34970.88661.3733-0.10320.06750.0157-0.18450.0419-0.0494-0.44140.02730.06130.1746-0.0374-0.0250.08150.0210.09130.8839-9.0229-155.3672
281.06430.31690.44121.18630.98392.54720.0462-0.026-0.11410.36220.0689-0.21270.0610.1311-0.11510.1845-0.0067-0.08940.08010.02860.152910.1316-18.7486-139.0792
295.1077-4.8279-2.626114.68417.06284.54990.0329-0.3497-0.38160.9244-0.09590.34160.3565-0.58770.06290.3598-0.0094-0.01040.33380.09320.06551.9634-15.564-131.8209
300.56220.15010.57371.58691.24421.7893-0.03430.0513-0.12920.17660.1301-0.2342-0.10590.1586-0.09580.1625-0.0212-0.05270.13340.01260.18998.3585-17.3481-146.561
311.9042-1.8066-0.63533.6683-3.698912.9277-0.0037-0.26490.17510.09330.36480.2525-0.6695-0.5206-0.36110.13640.0975-0.02090.1236-0.03130.2654-20.291552.2553-54.4015
322.7995-0.1891-0.30861.81750.24470.7301-0.11930.13190.1696-0.24450.1069-0.1361-0.30910.07130.01250.1902-0.01480.03040.12850.01480.1671-7.196846.9903-63.3445
331.0702-0.30370.36361.3008-0.00181.5318-0.0447-0.06470.0880.13950.01470.1023-0.1449-0.13120.030.0660.03390.03570.1096-0.00730.1301-14.53640.8635-50.9698
340.81160.00160.22961.37670.35841.31940.0018-0.0906-0.02980.11580.0331-0.00380.0398-0.0903-0.0350.07050.01880.03390.14060.00270.1314-11.866933.3354-53.5179
353.4671-0.6679-1.07271.97760.87253.0293-0.0492-0.14040.20040.36180.0629-0.2222-0.1390.0711-0.01370.13670.0198-0.00350.1114-0.00640.1025-7.445542.3776-44.2834
361.49311.49130.71242.52480.65351.7180.070.1938-0.1483-0.13940.1677-0.37750.19040.3091-0.23770.09060.05490.05520.1274-0.06250.1605-3.295515.4284-75.9364
371.47920.28190.23292.37980.46451.90330.0781-0.1127-0.10180.28430.0056-0.04170.2425-0.0213-0.08370.15070.0114-0.00580.09830.00670.1079-12.853912.6161-66.3645
381.05210.37020.93951.38381.05462.3596-0.00390.07440.0502-0.45530.00880.0636-0.3158-0.0275-0.0050.22380.02560.00480.08710.030.0806-16.258625.3694-85.8968
395.50885.7814-0.050114.22130.67880.09270.1042-0.2850.0409-0.4162-0.15790.604-0.0918-0.09630.05380.17070.1447-0.07770.49290.0410.1903-26.442420.4144-85.1984
400.35040.35490.50421.74380.90241.3722-0.00640.03730.0211-0.29710.0773-0.0302-0.1030.1064-0.0710.13320.01050.03310.12830.0030.0983-11.737324.1169-79.5537
410.30970.41690.35724.0201-1.0751.12270.09810.0118-0.11730.489-0.1352-0.55030.01290.09470.03710.28770.0615-0.11940.13250.0020.1929-10.6002-12.2373-181.7832
421.21640.7769-1.69666.5364-0.47652.435-0.0365-0.1599-0.0082-0.09240.1358-0.77940.03450.2856-0.09930.0040.0237-0.00010.2682-0.0530.3634-0.7747-3.6528-197.8021
430.43770.02130.1172.46270.41861.76890.04030.0084-0.05970.40590.0604-0.20810.13020.0498-0.10080.11790.0366-0.04810.09070.00510.0956-15.8969-8.6362-189.1171
440.1850.02890.21912.59980.0060.99120.0310.0651-0.0520.03290.0774-0.11060.0891-0.0287-0.10840.08230.0152-0.01090.1381-0.01310.1268-18.2883-6.7607-198.513
458.04554.2771-6.78412.3033-3.42036.9148-0.0205-0.0866-0.58270.09530.0008-0.38810.73040.35250.01960.43970.155-0.26210.0977-0.09770.2667-16.3267-22.3926-192.178
461.2317-1.50680.0842.65161.1041.90360.09510.16250.2011-0.3827-0.1121-0.2061-0.28530.16530.01690.244-0.00090.01360.15580.03980.105-25.114724.7595-209.7104
472.5308-1.2311-0.76546.12610.34930.23610.07070.16430.2062-0.38340.0061-0.6318-0.03-0.0181-0.07680.0857-0.03520.12610.2637-0.00360.2459-6.903418.6952-206.4831
480.7346-0.03580.44671.81190.19541.14330.01910.0201-0.0262-0.0750.0002-0.0265-0.083-0.0169-0.01940.07290.01020.0310.12810.00720.0871-23.622420.5697-198.7988
499.3581-3.43881.53647.9709-1.12263.0838-0.0138-0.032-0.14590.2206-0.06270.307-0.0142-0.2590.07650.11620.02050.05040.1501-0.02890.0511-28.588428.5086-186.1799
500.7828-0.45230.47831.92480.2940.7871-0.05150.02150.02450.01520.0474-0.2382-0.16330.06740.00410.0944-0.01260.0230.14280.00130.1282-17.366221.7868-195.7178
510.5171.2209-0.23464.8030.90877.4822-0.0334-0.1859-0.13090.47220.0431-0.46710.62420.5095-0.00980.34760.1041-0.12810.20330.04460.158424.695341.9434-94.1301
521.6335-0.5197-1.59271.82221.22255.04850.0248-0.03480.15320.19650.1322-0.48410.14230.4517-0.15690.12320.0116-0.06230.1212-0.00090.182928.935349.6318-106.1677
530.66290.16550.48782.14620.22241.20630.1053-0.1659-0.06670.40370.002-0.08930.2229-0.1312-0.10730.2549-0.0217-0.05020.0960.03220.049617.677843.6432-97.3701
540.28890.01760.34052.95050.27521.15470.0945-0.0197-0.04810.0561-0.02260.10640.2297-0.1044-0.07190.2184-0.0235-0.05120.09640.01960.081413.75239.5517-110.8659
551.9760.0460.23571.9489-0.2681.90650.2328-0.0417-0.18630.0855-0.0853-0.30710.45210.2293-0.14750.32690.0218-0.10460.04740.00750.11221.206631.4398-106.7836
563.2777-1.98162.073315.822119.977632.9970.4279-0.91820.3376-0.8663-0.29860.2566-0.0488-1.5489-0.12920.46580.0409-0.37660.375-0.23941.0203-1.672971.4244-126.2386
5712.30373.384-0.73436.1092-0.90673.9603-0.19620.57760.6316-0.87150.10730.2353-0.26640.19090.08890.4641-0.0047-0.10980.06020.03480.05839.343164.6927-132.6023
580.68890.06040.4012.16660.35741.4726-0.11540.03070.0256-0.4282-0.01130.1604-0.2307-0.06870.12670.22010.0174-0.0950.04930.00750.05359.417565.8665-121.3817
590.3148-0.19220.53362.75740.24491.3142-0.128-0.08290.0506-0.11780.01630.0944-0.2241-0.0760.11170.20320.0138-0.06860.0943-0.00450.09912.421468.0847-113.2186
608.10010.036-2.98210.7302-2.12647.2231-0.13890.2950.57970.17020.1257-0.0585-0.4951-0.42820.01330.44640.1358-0.21570.10850.0010.17673.07581.0472-120.7154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 29
2X-RAY DIFFRACTION2A30 - 74
3X-RAY DIFFRACTION3A75 - 113
4X-RAY DIFFRACTION4A114 - 146
5X-RAY DIFFRACTION5A147 - 230
6X-RAY DIFFRACTION6B23 - 43
7X-RAY DIFFRACTION7B44 - 113
8X-RAY DIFFRACTION8B114 - 159
9X-RAY DIFFRACTION9B160 - 172
10X-RAY DIFFRACTION10B173 - 230
11X-RAY DIFFRACTION11C23 - 51
12X-RAY DIFFRACTION12C52 - 96
13X-RAY DIFFRACTION13C97 - 132
14X-RAY DIFFRACTION14C133 - 149
15X-RAY DIFFRACTION15C150 - 230
16X-RAY DIFFRACTION16D23 - 44
17X-RAY DIFFRACTION17D45 - 113
18X-RAY DIFFRACTION18D114 - 146
19X-RAY DIFFRACTION19D147 - 222
20X-RAY DIFFRACTION20D223 - 230
21X-RAY DIFFRACTION21E23 - 34
22X-RAY DIFFRACTION22E35 - 90
23X-RAY DIFFRACTION23E91 - 146
24X-RAY DIFFRACTION24E147 - 215
25X-RAY DIFFRACTION25E216 - 230
26X-RAY DIFFRACTION26F23 - 43
27X-RAY DIFFRACTION27F44 - 113
28X-RAY DIFFRACTION28F114 - 164
29X-RAY DIFFRACTION29F165 - 172
30X-RAY DIFFRACTION30F173 - 230
31X-RAY DIFFRACTION31G23 - 35
32X-RAY DIFFRACTION32G36 - 78
33X-RAY DIFFRACTION33G79 - 145
34X-RAY DIFFRACTION34G146 - 210
35X-RAY DIFFRACTION35G211 - 230
36X-RAY DIFFRACTION36H23 - 60
37X-RAY DIFFRACTION37H61 - 113
38X-RAY DIFFRACTION38H114 - 164
39X-RAY DIFFRACTION39H165 - 172
40X-RAY DIFFRACTION40H173 - 230
41X-RAY DIFFRACTION41I23 - 41
42X-RAY DIFFRACTION42I42 - 59
43X-RAY DIFFRACTION43I60 - 145
44X-RAY DIFFRACTION44I146 - 219
45X-RAY DIFFRACTION45I220 - 230
46X-RAY DIFFRACTION46J23 - 43
47X-RAY DIFFRACTION47J44 - 58
48X-RAY DIFFRACTION48J59 - 164
49X-RAY DIFFRACTION49J165 - 172
50X-RAY DIFFRACTION50J173 - 230
51X-RAY DIFFRACTION51K23 - 43
52X-RAY DIFFRACTION52K44 - 70
53X-RAY DIFFRACTION53K71 - 129
54X-RAY DIFFRACTION54K130 - 209
55X-RAY DIFFRACTION55K210 - 230
56X-RAY DIFFRACTION56L23 - 29
57X-RAY DIFFRACTION57L30 - 43
58X-RAY DIFFRACTION58L44 - 145
59X-RAY DIFFRACTION59L146 - 222
60X-RAY DIFFRACTION60L223 - 230

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more